rs719871

Variant names:

• chr10-78385678-C-T
• rs719871
• ENST00000421324.4:n.51-143073C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421324.4(ENSG00000282863):​n.51-143073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,172 control chromosomes in the GnomAD database, including 867 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (867 hom., cov: 32)
• Consequence: ENSG00000282863 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

ENSG00000282863 (HGNC:):

LINC00595 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282863	ENST00000421324.4	n.51-143073C>T		intron_variant	Intron 1 of 2	1
LINC00595	ENST00000624665.3	n.331+136608C>T		intron_variant	Intron 1 of 3	2
LINC00595	ENST00000634389.1	n.408-10733C>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16075 AN: 152054 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.106

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.106 AC: 16098 AN: 152172 Hom.: 867 Cov.: 32 AF XY: 0.108 AC XY: 7998 AN XY: 74374

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.105

Alfa AF: 0.106 Hom.: 420

Bravo AF: 0.106

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs719871; hg19: chr10-80145435;